Manipulate node features in a GraphSpace object — gs

Utilities for extracting and adding node-associated features stored in the fdata container of a GraphSpace object.

Usage

gs_fetch_features(x, vars = NULL, as_df = FALSE)

gs_add_features(x, data)

Arguments

x: A GraphSpace object.
vars: Character vector specifying feature names to extract. If NULL, all features are returned.
as_df: Logical. If TRUE, returns a data.frame. Otherwise returns the original backend representation.
data: A matrix-like or data.frame object containing node features. Rows must correspond to node identifiers.

Value

gs_fetch_features() returns a matrix-like object or data.frame containing the selected node features.
gs_add_features() returns a modified GraphSpace object.

Examples

library(RGraphSpace)

# Load a demo igraph and create a GraphSpace object
data('gtoy1', package = 'RGraphSpace')
gs <- GraphSpace(gtoy1)
#> Validating the 'igraph' object...
#> Ignoring graph-level attributes: 'name', 'mode', 'center'
#> Creating a 'GraphSpace' object...

# A feature matrix with node identifiers as row names
feats <- matrix(as.numeric(seq_len(gs_vcount(gs) * 3)), ncol = 3,
  dimnames = list(names(gs), c("geneA", "geneB", "geneC")))

# Add features (rows are matched and reordered to the nodes)
gs <- gs_add_features(gs, feats)
gs_features(gs)
#> [1] "geneA" "geneB" "geneC"

# Fetch all features, or a subset as a data.frame
gs_fetch_features(gs)
#> 5 x 3 Matrix of class "dgeMatrix"
#>    geneA geneB geneC
#> n1     1     6    11
#> n2     2     7    12
#> n3     3     8    13
#> n4     4     9    14
#> n5     5    10    15
gs_fetch_features(gs, vars = c("geneA", "geneC"), as_df = TRUE)
#>    geneA geneC
#> n1     1    11
#> n2     2    12
#> n3     3    13
#> n4     4    14
#> n5     5    15